When the crew learn that the ship is set to automatically return to Earth they are clearly disturbed by this. What is Earth like at this time in the Alien story? What has happened to Earth to make them so afraid of returning there?

I think they are reluctant to return to Earth just because they are smugglers involved in all kinds of illegal activities.
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Laurent PireynJan 18 '12 at 11:27

Ripley gave her life trying to save Earth. Her fear was that the company would bring the aliens back, and that they would be to dangerous to control. In resurrection she is reborn as the hybrid who no longer fears the aliens. The idea that Earth is a lost cause makes her more empathetic to the aliens. The deformed mutations in the lab, and the dislike for Earth all point to "man being his own worse enemy". It's not the best plot line in the movie series.
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Mathew FoscariniNov 8 '12 at 20:12

But well, if Earth is such a delsolate place, why not let the Aliens have their share of it. This Mad Max-Wasteland doesn't really fit into the picture of Earth as the center of human civilization (or at least government), that I got from the movie's dialogue. Maybe this is the reason for deleting this scene. But good answer, though.
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Napoleon Wilson♦Jan 18 '12 at 16:02

Great! thanks for the link to the deleted scene!
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undefinedJan 19 '12 at 10:50

I believe that they blew up the ship ultimately to stop the possibility of an alien infestation from occurring on earth. This has always been Ripley's mission in the previous films...therefore her Human half took over in the end.